Phylogeny and Genomic Inference for Quantitative Traits It is proposed to develop statistical methods for analyzing data on phenotypic traits within populations, between populations, and between species, in an integrated way. Computer programs will be written and distributed to allow us to compare inferences at these levels and test whether divergence of characters among species shows different patterns of divergence when compared to the same characters observed between populations. Discrete 0/1 traits will be handled as well as quantitatively measurable traits. For the discrete traits, the threshold model of quantitative genetics will be used. Simple models of change of measurable environmental variables will be incorporated as well to allow testing of effects of these environments. These methods will be extended to also be able to handle neutral markers such as SNPs from genomic sequences. The pattern of variation within and between species of these SNPs creates opportunities to test for natural selection, by looking for combinations of characters that have evolved with a noticeably different pattern of covariation than the markers. In this way the testing framework will begin to unify population biology inferences with genomic methods, as genomic methods are increasingly applied to the biology of natural populations.